Is Viome a revolutionary technology poised to “make sickness optional” or is it a work-in-progress that will need to bake a little before it becomes truly useful?

Let me start with the answer to the question everyone asks first: is Viome a scam?

My answer is an emphatic no. I’ve followed the company from the beginning, met with their top execs and scientists, tested (and paid for) the product myself multiple times, and I’m convinced they’re the real deal. As a microbiome enthusiast who’s conducted more than 600 tests on myself over the years, I’m proud to have had a front row seat with all of the top testing companies and labs, including a short stint at the now-bankrupt uBiome. I’m convinced that the people at Viome genuinely share my passion for the incredible potential of this new and emerging science, and like me, they sincerely want this technology to be widely available to normal consumers, at reasonable prices. We don’t want to wait!

But it’s certainly possible for even the most well-intentioned companies to get ahead of themselves with technology. Is that the case with Viome?

Microbiome overview

The theory is intriguing: your body is covered within and without with microbes, collectively responsible for 10x the number of human genes you inherited from your parents, and those microbes — collectively referred to as the microbiome — have been shown over and over to have many intriguing associations with just about every human condition, from allergies and Alzheimers to mental health and of course a plethora of different gut issues.

Thanks to some miracles of modern technology, it’s become possible over the past ten years to read those microbial genes. The most popular method, often called “16S”, uses a blunt shortcut to give a rough overview of the major families of microbes present in a sample. Because of its low cost and lengthy history, most of the earliest and most pathbreaking discoveries were made using this technology, and it’s still popularly used in an overwhelming number of research studies as a means to get the overall picture of a microbiome. The technology is easy and cheap — nearly any university lab can do it. You as a consumer can get 16S sequencing results in a few weeks for under $100 from companies like Thryve, Psomagen, and many others

A newer, more complex and expensive technology called “metagenomic” or “whole-genome sequencing” (WGS), is much more detailed than 16s and is the preferred method for top labs at the cutting edge of microbiome science, or for consumers willing to shell out more money: about double the time and price. This technology can see individual species in the sample, even those that differ by just a few DNA letters, which is often the difference between a deadly pathogen and an innocent bystander. To use an analogy in our more familiar human-sized world, a 16S test can reliably tell that you a mammal in your back yard, but you’d need WGS to tell whether it’s a dog or a wolf.

What is Transcriptomics and what do we know about it?

Both WGS and 16S suffer from a fundamental limitation: although they can identify with various degrees of precision the names of the microbes in your gut, they say very little about what those microbes are actually doing. To continue the back yard analogy, even if you know it’s a dog and not a wolf, your reaction will be very different depending on whether the dog is playing happily, sleeping, growling, or dead. Similarly, when trying to take action with your health, knowing which genes are present is no substitute for knowing what the genes are doing. In microbiology, you measure gene activity by the proteins they transcribe — also known as the transcriptome — and transcriptomics is the most state-of-the-art microbiome testing that aims to do just that.

Several top labs have begun to dabble in transcriptomics, but none of the leading scientists I talked to thinks the technology is possible in an at-home, consumer test. RNA is too unstable, they say. Even in perfect lab conditions, doing it right costs many hundreds, perhaps as much as a thousand dollars per sample.

That’s why Viome’s claims are so revolutionary. If true, they’ve solved two huge problems: state-of-the-art technology and consumer-level pricing.

Clinical Trials

In fact, they’ve had to solve another problem: how to interpret the sequencing results. Even if Viome has mastered the technical details for accurately sequencing an at-home, self-collected sample, the technology is so new that even the best labs aren’t sure how to interpret the data. Here’s where I am most impressed with Viome’s can-do attitude.

Most of the scientific reports you see about the microbiome come from research studies performed under grants funded by government agencies like the National Institutes of Health, charities like the Gates Foundation, or at universities like MIT. Often working under frugal, underfunded conditions, these scientists are thrilled when they can do a trial on just a few dozen subjects. But Viome’s founder, Naveen Jain, is a high tech startup veteran who follows the Silicon Valley playbook of “moonshots” — go big or go home projects that, if successful, will reap such huge rewards that the danger is dreaming too small, not too big. He and his co-founders realized early on that microbiome science requires large amounts of data, which means large trials.

Then they did what you or I would do if money were not the object and all you care about is collecting lots of high quality data. They recruited 1000 subjects — an order or two magnitude greater than typical microbiome studies — each of whom was given a before/after medical check including full blood tests, two weeks of high-tech continuous glucose monitoring and activity tracking, plus home delivery of specially-chosen foods to let the scientists find exact correlations between all these variables and the precise diet of the participants^[Glucose Response Study Instruction to Participants - Google Docs.pdf]. This is another reason I don’t believe Viome is a scam. If they were only interested in marketing, they could have done a study on 10 or even 100 people for a fraction of the cost and still made the same boasts. The only reason to do a full 1000 person study is … to find real, scientifically valid results.

And they did find scientifically valid results. Lots of them.

Their initial pre-print^[https://www.biorxiv.org/content/10.1101/641019v3] showed that they were able to predict glycemic response based on microbiome data alone. While this result wasn’t new — a team from Israel had demonstrated the same thing previously, founding Viome competitor DayTwo in the process — that they were able to replicate another lab’s results using transcriptomics technology was an important win.

But this wasn’t the only association they found between health and the microbiome. Their scientists were able to predict numerous other health conditions, including diabetes, irritable bowel syndrome, depression, and even cancer ^[see November 2019 presentation by Guru Banavar at Exponential Medicine on Youtube: https://youtu.be/7eFkT-wtznk?t=6487 (offline)] Their model, they said, could reliably identify other features too, like sleeping patterns, age, type of bowel movement, and more. Most importantly, they claimed they could tell exactly how one person’s transcriptome deviates from a healthy average and give specific dietary interventions that would put the person back on track.

My Experience: my first brush with digestive trouble

I’m fortunate that for most of my life I’ve been in overall good health, and my first two Viome tests confirmed that. Although the results suggested a few areas for optimization, I didn’t feel compelled to obey the advice because, well, the foods they recommended either didn’t appeal to me, or the ones they suggested I avoid were too convenient for me to give up. Why bother if I’m feeling pretty good even without their advice?

This all changed in April when I found myself suddenly undergoing laporoscopic surgery for a bowel obstruction, in my case caused by leftover scar tissue (“adhesions”) from a childhood appendectomy. Bummer. I was out of the hospital within days, fully expecting to go right back to my normal life of omnivore eating, when for the first time in my life I found myself facing serious gut issues.

Just a few bites of food made me feel uncomfortably full, and an hour or so later my stomach would tighten, my belly feeling like the surface of a drum. Soon I’d feel (and hear) intense gurgling, my intestines writhing painfully, a discomfort that lying down and rest couldn’t relieve. Some foods seemed better than others — bone broth soup, plain scrambled eggs — but these were outnumbered by other plain and seemingly healthy foods like oatmeal or yogurt. My painful reaction to food caused me to lose weight, and within a week or two I was seriously worried that my recovery might not happen.

Fortunately I had a few gut kits on hand, one from Viome and another metagenomic (WGS) kit from Psomagen. I promptly tested myself one morning and mailed both kits back to their labs.

Small Intestine Bacterial Overgrowth (SIBO)

While waiting on the results, my doctor noted that my symptoms met the classic definition of SIBO, small intestinal bacterial overgrowth, a condition not uncommon after surgeries like mine. The antibiotic given before my operation was absolutely necessary to prevent worse complications, but in killing microbes throughout my gut, it may have inadvertently left an opening for some otherwise benign bacteria to colonize the upper part of my intestine, the area that follows the stomach opening and should normally be mostly bacteria-free. Once the SIBO microbes gain a foothold, they can ferment the undigested food as it passes by, generating gaseous molecules that, when combined, cause the intestines to expand painfully, giving me that sense of “fullness” and discomfort as the gas bubbles make their way through the digestive tract.

Although there is wide agreement that SIBO is behind many digestive issues, the difficulty of directly reaching the upper intestine makes it hard to diagnose with absolute certainty. Short of directly inserting a probe deep into into the gut, SIBO must be tested indirectly, by measuring the levels of gases in the breath and comparing to healthy individuals. You can buy a home test kit for about $200, with results returned in about a week. You can get same-day results if there is a specialist clinic in your area, but in the middle of a pandemic on a weekend that wasn’t an easy option for me.

With any diagnostic test, the first question you should ask is what you will do with the results. Because of the indirect nature of the breath test, you can’t be certain that the results either confirm or disprove the presence of out-of-place microbes in the upper intestine, but the initial treatment for SIBO is so easy, you may as well try it even without a test. That was the obvious conclusion: try eating a SIBO-friendly diet for a few days and see if it helps. If I still feel uncomfortable, I can try other treatments, but there’s a chance that I’ll get immediate relief, so what do I have to lose?

You’ll find many SIBO-friendly diet suggestions on the internet, but they all agree on the need to avoid foods that are easy for bacteria to digest and ferment. Unsurprisingly, this includes nearly all heavily processed foods like sweets, especially sweetened beverages, bread made from refined flour, and most breakfast cereals. Many other simple sugars are off-limits too, including most fresh dairy as well as many fruits like apples. Instead they recommend fatty foods like eggs or coconut, and most basic proteins like plain chicken, fish, or tofu. Less obvious is the need to stay away from fiber, but that makes sense when you remember that SIBO microbes are in the wrong part of the long intestinal tract: fiber is good when it’s at the very end of the digestive process, but it’s not what you need at the beginning.

Although all SIBO diets agree on these basics, there are several variations. I quickly settled on the FODMAP diet^[technically I should call this the low FODMAP diet, because the point is to minimize the foods], because I noticed that their list of “bad” foods mapped well to what had been causing me trouble — bananas, for example, which I already had scrapped after it was obvious they were bad. FODMAP, an acronym that describes the categories of chemicals that are off-limits on the diet, has been well-studied, especially by scientists at Monash University in Australia, and you can find many resources on the internet and in the App Store that identify specific foods.

FODMAP Eating

Once I rid myself of the FODMAP-forbidden foods, I noticed immediate relief. And when I say “immediate”, I mean it really was dramatic. It turned out that many of the foods that ordinarily I considered healthy are terribly bad for SIBO: anything with dairy, including whey protein for example, fermented foods like kombucha or sauerkraut, avocados, and many others. Even a small amount of hummus or avocado, which ordinarily I thought was safe, would bloat me for hours afterwards. Simply stopping those foods made me feel much better. Meanwhile, the FODMAP “safe” foods like eggs, leafy greens, unseasoned chicken or fish — I found I could eat as much as I liked, so long as they weren’t seasoned with the off-limit spices like onions or garlic.

Rarely have I seen such an immediate and obvious turnaround. Simply by sticking to the good foods and avoiding the bad — which wasn’t all that hard, I found — I never had another gut problem again. In fact, the results were so good that within a week I decided to risk eating small amounts of the “bad” foods and within a few days of slow reintroduction, I found I was able to tolerate everything just like before. Whatever the condition I had been suffering — SIBO or something else — it was over and I felt great. I could finally go back to eating omnivorously, whatever I wanted, including dairy, wheat, ice cream — you name it.

Microbiome test results

It took several more weeks before the microbiome test results arrived. In my case, I appeared to have solved my problem using fairly generic advice I got from the internet fo free, but I was eager to learn what the microbiome-based, personalized advice would say. Since I know one diet that appears to work, wouldn’t it be amazing if the microbiome advice turned out to be similar?

Unfortunately, the results were mixed. Although many of the recommendations were similar, the diets disagreed on several important foods.

For example, both said I could eat peanuts and blueberries but should skip bananas. Both rejected garlic and onions as well as a number of vegetables including cauliflower and sweet potato. Both agreed I can enjoy whatever cheese I like, or many vegetables like carrots, eggplant, greenbeans and seaweed.

But the list of disagreements is long: mushrooms, honey and maple syrup, pears and apples, many vegetables including asparagus, Brussels sprouts

Dairy was especially notable. Viome says ‘enjoy’ to a glass of cow milk, which is strictly rejected by FODMAP. Similarly, Viome says both wheat and rye bread are fine as long as they are sprouted, but a FODMAP diet says no to almost all grains, except rice, which is forbidden by Viome.

Since I deliberately avoided anything forbidden by the FODMAP diet, I can’t say that all the recommended Viome foods wouldn’t work, but my gut felt much better after I gave up dairy and wheat. My mornings were much better after I switched to almond milk instead of cow milk for my daily latte. On the other hand, after FODMAP gave me the green light, I ate a lot of eggs and white rice without any difficulty, although both are strongly discouraged by Viome. Same thing with many other low FODMAP foods Viome said I should minimize (spinach, potato) or avoid entirely (eggs, cabbage) — I had been hungrily devouring them with no trouble for weeks before the Viome results arrived.

Psomagen’s arrived in 3 weeks, and Viome was a little more than 4.

On FODMAPs I had no trouble with

Meanwhile, I noticed digestive problems when I ate many of the foods Viome said I should enjoy (milk, chickpeas)